add option for FASTA file

NOTES

@@ -0,0 +1,4 @@
+We have use script to convert fasta to fastq downlaoded from here
+https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/fasta-to-fastq/fasta_to_fastq.pl
+
+

fasta_to_fastq.pl

@@ -0,0 +1,47 @@
+#Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI ([email protected])
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files 
+#(the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, 
+#merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is 
+#furnished to do so, subject to the following conditions:
+
+#The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 
+#OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE 
+#LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR 
+#IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+#!/usr/bin/perl
+use strict;
+
+my $file = $ARGV[0];
+open FILE, $file;
+
+my ($header, $sequence, $sequence_length, $sequence_quality);
+while(<FILE>) {
+        chomp $_;
+        if ($_ =~ /^>(.+)/) {
+                if($header ne "") {
+                        print "\@".$header."\n";
+                        print $sequence."\n";
+                        print "+"."\n";
+                        print $sequence_quality."\n";
+                }
+                $header = $1;
+		$sequence = "";
+		$sequence_length = "";
+		$sequence_quality = "";
+        }
+	else { 
+		$sequence .= $_;
+		$sequence_length = length($_); 
+		for(my $i=0; $i<$sequence_length; $i++) {$sequence_quality .= "I"} 
+	}
+}
+close FILE;
+print "\@".$header."\n";
+print $sequence."\n";
+print "+"."\n";
+print $sequence_quality."\n";
+

needle.sh

@@ -4,6 +4,8 @@ source $(dirname $0)/argparse.bash || exit 1
 argparse "$@" <<EOF || exit 1
 parser.add_argument('bam')
 parser.add_argument('outdir')
+parser.add_argument('-fasta', '--fasta', action='store_true', default=False,
+                    help='Forse [default %(default)s]')
 parser.add_argument('-f', '--force', action='store_true', default=False,
                     help='Forse [default %(default)s]')
 EOF
@@ -59,14 +61,25 @@ SAMPLE=${OUTDIR}"/"${prefix}
 
 
 echo "Extract unmapped reads from " $BAM
+if [[ $FASTA ]]
+then
+perl ${DIR_CODE}/fasta_to_fastq.pl $BAM > ${SAMPLE}.cat.unmapped.fastq
+else
+
 samtools view -f 0x4 -bh $BAM | samtools bam2fq - >${SAMPLE}.unmapped.fastq
-#samtools view -bh $BAM NC_007605 | samtools fastq - > ${SAMPLE}.NC_007605.fastq
-#rm -fr ${SAMPLE}.NC_007605.fastq
-#cat ${SAMPLE}.unmapped.fastq ${SAMPLE}.NC_007605.fastq>${SAMPLE}.cat.unmapped.fastq
-#rm -fr ${SAMPLE}.unmapped.fastq
-UNMAPPED=${SAMPLE}.unmapped.fastq
+samtools view -bh $BAM NC_007605 | samtools fastq - > ${SAMPLE}.NC_007605.fastq
+rm -fr ${SAMPLE}.NC_007605.fastq
+cat ${SAMPLE}.unmapped.fastq ${SAMPLE}.NC_007605.fastq>${SAMPLE}.cat.unmapped.fastq
+rm -fr ${SAMPLE}.unmapped.fastq
+
+fi
+
+
+UNMAPPED=${SAMPLE}.cat.unmapped.fastq
 
+wc -l $UNMAPPED
 
+exit 1 
 
 bwa mem -a ${DB}/viral.vipr/NONFLU_All.fastq $UNMAPPED | samtools view -S -b -F 4 - | samtools sort - >${SAMPLE}.virus.bam
 bwa mem -a ${DB}/fungi/fungi.ncbi.february.3.2018.fasta $UNMAPPED | samtools view -S -b -F 4 - |  samtools sort - >${SAMPLE}.fungi.bam

toy.example.fasta

@@ -0,0 +1,14 @@
+>1
+TCGCACCGGGGATCCTAGGCTTATTATATTGCGCTTTGTATTGAAGTCTGTTCTGTGTGGACTGACCTCAGCACAAGTGTTATGGGGCAGATCATAACAATGTTTGAGGCCCTGCCTCACATTATCGATGAGGTCATCAACATTGTTATAATAGTGCTTATAATAATAACAAGCATAAAGGCTGTGTACAACTTTGCTACCTGTGGCATCATTGCATTGATCAGCTTCTGCTTCTTGGCTGGAAGGTCTTGTGGCTTGTATGGTGTCTCTGGCTCTGACATTTACAAGGGACTCTACCAGTTCCAGTCCGTAGAGTTCAACATGTCACAATTGAATTTAACAATGCCCAATGCGTGCTCAGCCAACAATTCCCACCATTACATCAGCATGGGAAAATCTGGCCTGGAACTAACCTTTACAAATGACTCCATCATTCAACACAACTTCTGCAACCTAACTGATGGGTTCAAGAAAAAAACCTTTGATCATACACTTATGAGCATAGTGTCAAGCCTGCACCTGAGCATTAGAGGAAATACCATCTACAAAGCTGTGTCCTGTGACTTCAACAATGGGATTACAATCCAGTACAACCTAACCTTCTCTGATGCACAAGGTGCCATCAATCAATGTGGAACCTTCAGAGGTAGAGTTTTAGATATGTTTAGAACAGCTTTTGGGGGGAAATACATGAGGTCTGGCTATGGTTGGAAAGACTCCAATGGGAAGACAACCTGGTGCAGTCAAACCAACTATCAATACCTAATCATACAGAACAGGACATGGGAAAATCACTGTGAGTATGCCGGTCCTTTTGGTCTCTCAAGAATTCTTTTTGCTCAGGAGAAAACAAAGTTTCTCACTAGAAGATTGGCAGGGACTTTTACCTGGACATTGTCGGATTCTTCGGGAACTGAAACCCCAGGTGGGTATTGTCTGACAAGGTGGATGCTCATAGCTGCTGATCTCAAGTGTTTCGGGAACACAGCAGTTGCCAAATGCAACATCAACCATGATGAAGAATTTTGTGACATGTTGAGGTTAATTGACTATAACAAAGCCGCTCTAAAGAAATTCAAAGAAGACGTAGAGTCTGCCCTTCACTTGTTCAAAACAACTG
+>2
+CCGGGGATCCTAGGCTTATTATATTGCGCTTTGTATTGAAGTCTGTTCTGTGTGGACTGACCTCAGCACAAGTGTTATGGGGCAGATCATAACAATGTTTGAGGCCCTGCCTCACATTATCGATGAGGTCATCAACATTGTTATAATAGTGCTTATAATAATAACAAGCATAAAGGCTGTGTACAACTTTGCTACCTGTGGCATCATTGCATTGATCAGCTTCTGCTTCTTGGCTGGAAGGTCTTGTGGCTTGTATGGTGTCTCTGGCTCTGACATTTACAAGGGACTCTACCAGTTCCAGTCCGTAGAGTTCAACATGTCACAATTGAATTTAACAATGCCCAATGCGTGCTCAGCCAACAATTCCCACCATTACATCAGCATGGGAAAATCTGGCCTGGAACTAACCTTTACAAATGAC
+>3
+TTTACAAGGGACTCTACCAGTTCCAGTCCGTAGAGTTCAACATGTCACAATTGAATTTAACAATGCCCAATGCGTGCTCAGCCAACAATTCCCACCATTACATCAGCATGGGAAAATCTGGCCTGGAACTAACCTTTACAAATGACTCCATCATTCAACACAACTTCTGCAACCTAACTGATGGGTTCAAGAAAAAAACCTTTGATCATACACTTATGAGCATAGTGTCAAGCCTGCACCTGAGCATTAGAGGAAATACCATCTACAAAGCTGTGTCCTGTGACTTCAACAATGGGATTACAATCCAGTACAACCTAACCTTCTCTGATGCACAAGGTGCCATCAATCAATGTGGAACCTTCAGAGGTAGAGTTTTAGATATGTTTAGAACAGCTTTTGGGGGGAAATACATGAGGTCTGGCTATGGTTGGAAAGACTCCAATGGGAAGACAACCTGGTGCAGTCAAACCAACTATCAATACCTAATCATACAGAACAGGACATGGGAAAATCACTGTGAGTATGCCGGTCCTTTTGGTCTCTCAAGAATTCTTTTTGCTCAGGAGAAAACAAAGTTTCTCACTAGAAGATTGGCAGGGACTTTTACCTGGACATTGTCGGATTCTTCGGGAACTGAAACC
+>4
+AACCGGCGCCAGTGTGCTGGGACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAAACCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACAC
+>5
+CATACCTAATCAAAACCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCACATACCTAATCAAATCCGTACACCCCGCTCCTCCCTTTCTGGTAATTTTACTTTTATTTTTTTCATTTTTTTATTTTTTCATTTTTTCATTTTTTCATTTTCTCATTTTCTCTTTTTTAATCACTCTAGACGGATTTCCTCTTCTGGTAATTTTCTTTTTCTCATTTTCTCATTTTCTCATTTTCTCTTTTCTAATCACTCGAAACGGATTTCCTCTTTCGGTAATTTTGCTTCTTTGTTTTTTACTTTAATTTCTTTTTCCTCTTCTCCTCTTTCGCTTTCTCCTTTCACTCTCATCCATTCTCATTCCTCAATTTATACTTTTTTTGGCAGTATTCTTGACTGTTTTTCACCATTTCCCCTTACCCGCACTTCCATCACATTTTCTTTGTCAATCCACCTTCTTGCCATGGCCAATGCTTGGTCCTGCTGGGCCTGGTCCTTGCATAGGATACACACGTTACCCGCACAATTATCACCCATTTTCAACTTCTTCCAACTTTTGCTCCTCTTGCCATGAAACTTCATTTCAAATTACTTCACTTCATCACTTCCTTAGTTACCCTGCTTTATTATAAATCACGTGCTTCCCATCTCCCGCTTCCCATCTCCCGCTTCCCATCACCTGCTTCTCTTCACCTGCTTCTCTTCACTTTCATTTTTCATCCCTTCTCATTCTACCTTTCTTTCCCTCTCTCCCTCTGAATATAAGAATTCTCCACTGTTTTTCACAATTACTACTTACCCGCACTTAAACTACACTTCTCCATGTTAATCAACCT
+>6
+TAACCCTAACCCTAACCCTGACCCTAACCCTAACCCTAACCCTAACCCTAACCAGTACACGCGTACACGTACAAGCACCCGTACCCCCAGTATACCTGGACACCCGTACTCAGTTATCCTTTTTATTAGTGTACCCGCCTCTTGCACGCATGCCACAGTTCTTCAGCAGAAGAACACGCACAATGCTCTTTGATAAACGTGCGGACATGAAAAAAAGGGAAAAACGCAGCTACGTGTGCTGTCGTTGGTTTCACAGCGTCAAGCCGCGTCGGTGTACCAAAGAGGAGGTGACCCATCGAGTACTCGCACCCTCTAGCTCTCCTTTTCTGCCTCGTATTATACACGTTGATCGGAAAACAGGGTAGGCACTAGCCACCGATAATCTTCAATCGTACATCTGTCTGCGTAAGCGCGTGCCCCGGATGGAGGGCATGGAACTGCATCGACCGCCCACGGCGATCGCCGATCAGCCAGCGATGTGACTGCAACGCTGTTTGTTTCCACAACGAGGGCTGAAGGCTTTCTGATAGATTGTGCGCTATAGAACAAGGAGGGAGAGCCCACCCCTTTTTATGCGAAAACTCCTCACCCAAAGCAAGGAGGGCGGCGGGTGGGAAGCGGAAAGCCAACGCCCACGCGGACGCAATTAGCACCGACCGAAAACGAGCAGTGAGAAAAAGGGAAGTCTCTCAGACTGGGAAGAGATGAGCCGAGGAGATAAATGCACCAGATCCGAGGTACCGCGGCACAAGAGGAGCCGGGTGATATTTTTTGTTGTTTTCAGTGTTTCCTCGTGAGACGGCAAAACACGAGGCAGAAAAGGTG
+>7
+CTTCAGCAGAAGAACACGCACAATGCTCTTTGATAAACGTGCGGACATGAAAAAAAGGGAAAAACGCAGCTACGTGTGCTGTCGTTGGTTTCACAGCGTCAAGCCGCGTCGGTGTACCAAAGAGGAGGTGACCCATCGAGTACTCGCACCCTCTAGCTCTCCTTTTCTGCCTCGTATTATACACGTTGATCGGAAAACAGGGTAGGCACTAGCCACCGATAATCTTCAATCGTACATCTGTCTGCGTAAGCGCGTGCCCCGGATGGAGGGCATGGAACTGCATCGACCGCCCACGGCGATCGCCGATCAGCCAGCGATGTGACTGCAACGCTGTTTGTTTCCACAACGAGGGCTGAAGGCTTTCTGATAGATTGTGCGCTATAGAACAAGGAGGGAGAGCCCACCCCTTTTTATGCGAAAACTCCTCACCCAAAGCAAGGAGGGCGGCGGGTGGGAAGCGGAAAGCCAACGCCCACGCGGACGCAATTAGCACCGACCGAAAACGAGCAGTGAGAAAAAGGGAAGTCTCTCAGACTGGGAAGAGATGAGCCGAGGAGATAAATGCACCAGATCCGAGGTACCGCGGCACAAGAGGAGCCGGGTGATATTTTTTGTTGTTTTCAGTGTTTCCTCGTGAGACGGCAAAACACGAGGCAGAAAAGGTGCAAGAGATCCAGGTGGCTGGCGAAGAGGAGGAACATGAGAAGAGAGACAGTCAACATTGGCGGGGAGTCGAACTTTGTGCAGCTCATGTGTGCAGGTGCAGGTCGATGGATAGAAGGCTAAGAGGCGATAGGACAGGGTCCCTTCACACCACAAGCGTGAGTGATGGAGTTATATGCGCATGGTCGAATAGGTATGCACATGTACGGCAGACAGGAAAGTAGAAGAGAGGAATTCGGAGTTGTGGAGAACGGGAAGTCGATGGGGCAGCAGCAGCAGTCAGAGCAGCAGACGAAATGCTACACGGAACGGCTTCACGGAGAGAGCATATCAGAGAAGCAGGGGAGCTGAGAAGTGCAGTCGATGTGTCACGCTTTGAAGTGTGTGACAT