Entering edit mode
12 months ago
Hi all,
is there an easy way to filter a contig fasta file which looks like this by the depth stated in the identifier e.g. make a new file with contigs with depth <2.0? Thanks in advance :)
>1 length=282707 depth=1.00x
TACGAAAAAAAAGCAAAAAAAAGAGGAGGAGGCTCACGCCTCCCCCTCTCCCTTTCAGCTTACGCCACCA
GCACGTCAGTCCGCGTCAACAGCATGCCCGTCAATCGGCGCCCTTATGTTGGGACATGATCAATGACAGG
ACACCCGGAACTTGTCTTTGTGCAGGCCTGTCCTCATACGTAAGGGGCTTTGCATCCCGCATCGCAATGA
>2 length=26815 depth=3.45x
CCAGGGAAGCAGCAGTCAACACGCTAAAAACCTGAAATCAGGCACAAGAGAAGTCAATCAAAGGTTTTTC
GAACCCTCCAGGTTTGACCCCGCAAAAGACCTCGCCAACCAAAAAAAGCACAAACTGTCTCTGGCCTTTG
GCGACCGTATTTTCGAGGACGATAATCACCTGATCTTGCCCACCATCCGCATTGAGGATGAGGAGGATCG
>3 length=24243 depth=1.02x
CACTTTTTTCGAAAAAACAATCTCCGCCTGAATTCGGATCGCGGTTAACTGCCGATTTCGACGGGCATCT
TTTTATCGTCCCCTTACCAGCAGCACCAGACGAAGTGGTATAATATAACAATAATCCGTTGGGCAGGATA
ACTGCTATTATCAAAATCAGCGCAGACCCTGCCAAAGACGGCCCGTAATATGCGGCCATCGGGGAGCGGC
CGCCGTAGCTGTTACGCCGTACTGCCCCAATCCATGTTCCATTCAAGGCAAGAGACGCACAAACCGATGC
AACCTGCTCCCAAGGCAACACTTCTCACGCGGCTCAATGAACAGATCGCCGTCAAGATGACCTTCATTTT
TGGAAGCATCTGGTGCGTTTACGCCTTCCTTGTCTTCTCCCTGATCCCGCTTGCCGCACCGGGATGGCAG
It worked great - thanks Pierre