o Rŀg+4@s>dZddlmZddlmZddlmZddZd dd ZdS) a!Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools. You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences). This module contains a parser for the pairwise alignments produced by Bill Pearson's FASTA tools, for use from the Bio.AlignIO interface where it is referred to as the "fasta-m10" file format (as we only support the machine readable output format selected with the -m 10 command line option). This module does NOT cover the generic "fasta" file format originally developed as an input format to the FASTA tools. The Bio.AlignIO and Bio.SeqIO both use the Bio.SeqIO.FastaIO module to deal with these files, which can also be used to store a multiple sequence alignments. )MultipleSeqAlignment)Seq) SeqRecordcCs|d}t|d}t|dt|dkr*t|d|}t|d|d}n|t|d}|t|dd}||d7}|dksQ||ksQ|t|kr[td||||f|||S)a_Extract alignment region (PRIVATE). Helper function for the main parsing code. To get the actual pairwise alignment sequences, we must first translate the un-gapped sequence based coordinates into positions in the gapped sequence (which may have a flanking region shown using leading - characters). To date, I have never seen any trailing flanking region shown in the m10 file, but the following code should also cope with that. Note that this code seems to work fine even when the "sq_offset" entries are present as a result of using the -X command line option. -al_display_startal_startal_stoprz.Problem with sequence start/stop, %s[%i:%i] %s)stripintcountlen ValueError)alignment_seq_with_flanking annotationalign_stripped display_startstartendrG/var/www/html/myenv/lib/python3.10/site-packages/Bio/AlignIO/FastaIO.py_extract_alignment_regions    rNc #sd}d}d}d}d}d}d} f dd } |} d d d d iiii id d d } D]} d | vrx| d sx rPrP| V|} | | d dd d dd d iii id d d } q<| d r| |ksJrJrJrJ rJd usJ rJrJ| rJd q<| dvrˈ rr| V|} d d iii id d d } q<| d r d usJ| dd ddd ksJ| d usJrJrJ rJrJrJ r J| rJ|} q<| dr@ r!r!| Vii id d d } | dd d dd|} q<| drc rLsPJ| | Vii id d d } |} q<| dr| |kr d uswJ| d usJ|  | dd d ddsJ| |} q<| |krň d usJ| d usJ| | dd d ddsJ| |} q<| |krq.build_hspNrz>>>z!! No )z>>><<>>///z, z>>z>-->zstate %i got %rz ; al_consz; z: cs|]}|VqdSNr .0srrr 1z#FastaM10Iterator..)BiopythonParserWarningzMissing colon in line: csrJrKrLrMrrrrP=rQ z Bad line: zUnexpected state r!#commandz version versionz compares a rz searches a ) startswithfindr split RuntimeErrorwarningsBiorRwarnr)r> seq_countstate_PREAMBLE state_NONEstate_QUERY_HEADERstate_ALIGN_HEADERstate_ALIGN_QUERYstate_ALIGN_MATCHstate_ALIGN_CONSrHstatecons_seqlinekeyvaluer\rRrr;rFastaM10Iterator>s2"R       $         ( (    $  &                rlrK) __doc__ Bio.AlignrBio.Seqr Bio.SeqRecordrrrlrrrrs    "